Set up¶

Step 0 Import the needed libraries

In [965]:
#!pip install opencv-python
#!pip install keras-metrics
#!pip install spicy
#!pip install --upgrade tensorflow

This is where we tested the 2 step Model.¶

In Order to run this please follow the following steps:¶

    ## Run the imports
    ## Run the functions Download Images, then Copy Images.
    ## Create manually on your directory folders, we created them as img_3, imgPrueba, img_b, img_n, img_m
    ## Run creating_folder_test_spit()
    ## Run create_folder_3_parts()
    ## Create_Folder_Malignant()
    ## Create_Folder_B()
    ## Create_Folder_N()
    ## Run the rest of the function and then run Create_Images
    ## The inputs: Create_images(train_generator,'directory', 'train')
    ## also do it for test data. Do this for the directory for img_3, img_b, img_n, img_m
    ## The delete Image is just to delete but dont run it 
    ## Once you have all the images you can run everything in genertor sector in this same steps. This might take a lot of time. 
In [1]:
import pandas as pd
from sklearn.metrics import f1_score
import requests  
import tensorflow as tf
import seaborn as sn
import os, shutil
import numpy as np
import matplotlib.pyplot as plt
import cv2
from keras import backend as K
import tensorflow as tf
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense, Conv2D, Flatten, Dropout, MaxPooling2D

import pickle

from tensorflow.keras.preprocessing.image import ImageDataGenerator

from tensorflow.keras import models
from tensorflow.keras import layers
from tensorflow.keras import optimizers
from keras.preprocessing import image
import keras_metrics
from collections import Counter
import random
from spicy import ndimage
import imageio
from sklearn.pipeline import Pipeline
WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\losses.py:2976: The name tf.losses.sparse_softmax_cross_entropy is deprecated. Please use tf.compat.v1.losses.sparse_softmax_cross_entropy instead.

C:\Users\dggua\anaconda3\Lib\site-packages\paramiko\transport.py:219: CryptographyDeprecationWarning: Blowfish has been deprecated
  "class": algorithms.Blowfish,
In [2]:
import pandas as pd
import requests  
import seaborn as sn
import os, shutil
import numpy as np
import matplotlib.pyplot as plt
import cv2

import tensorflow as tf
from tensorflow.keras.models import Sequential, Model
from tensorflow.keras.layers import Dense, Conv2D, Flatten, Dropout, MaxPooling2D, BatchNormalization,Concatenate,Input

import pickle

from tensorflow.keras.preprocessing.image import ImageDataGenerator

from tensorflow.keras import models, layers, optimizers
from keras.preprocessing import image
import keras_metrics

from spicy import ndimage
import imageio

from tensorflow.keras.utils import Sequence, to_categorical

from keras.preprocessing.image import load_img, img_to_array

from PIL import Image
from sklearn.model_selection import train_test_split

from tensorflow.keras.optimizers import RMSprop

Step 1 Organize the images in their respective folders

In [3]:
df = pd.read_csv("fitzpatrick17k.csv")
data = df[df['url'].notna()]
data['label'].value_counts()

####################
three_part = data['three_partition_label'].unique()
d = data.loc[data['three_partition_label']=='benign']
print(three_part)
print(d['label'].unique())
['non-neoplastic' 'benign' 'malignant']
['dermatofibroma' 'syringoma' 'prurigo nodularis' 'nevocytic nevus'
 'porokeratosis of mibelli' 'milia' 'granuloma pyogenic' 'epidermal nevus'
 'naevus comedonicus' 'pilar cyst' 'congenital nevus' 'lymphangioma'
 'pilomatricoma' 'disseminated actinic porokeratosis' 'halo nevus'
 'fordyce spots' 'telangiectases' 'becker nevus' 'pyogenic granuloma'
 'port wine stain' 'nevus sebaceous of jadassohn' 'porokeratosis actinic'
 'seborrheic keratosis' 'mucous cyst']
In [4]:
def download_images():
    for i in range(0 ,len(data)):
        url = data['url'].iloc[i]
    label = data['label'].iloc[i]
    print(i)
    if url == '0':
        print('nan image')
    else:
        headers = {
            'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:55.0) Gecko/20100101 Firefox/55.0',
        }
        data_url = requests.get(url, headers=headers).content 
        m = 'C:/Users/dggua/Documents/DeepLearning/img/img'+str(i)+'.jpg'
        m = 'C:/Users/liita/OneDrive/Documentos/Nova IMS/Deep learning/Proyecto/Prueba/'+str(label)+'/img'+str(i)+'.jpg'
        f = open(m,'bw') 
        f.write(data_url) 
        f.close() 

def copy_images(source_folder, destination_folder):
    # Get a list of files in the source folder
    files = os.listdir(source_folder)
    # Iterate over files and copy images
    for file in files:
        # Check if the file is an image (you can customize this check based on your requirements)
        if file.endswith('.jpg'):
            source_path = os.path.join(source_folder, file)
            destination_path = os.path.join(destination_folder, file)
            shutil.copy(source_path, destination_path)
            print(f"Copied '{file}' to '{destination_folder}'")

#We create a folder where we are going to get the images, and they are classified by ['non-neoplastic' 'benign' 'malignant']
def create_folder_3_parts():
    # Example usage
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_3/'+name
        os.mkdir(m)
        for i in three_part:
            d = data.loc[data['three_partition_label']==i]
            labels_unique = d['label'].unique()
            mm = m + '/'+ i
            os.mkdir(mm)
            for l in labels_unique:
                l= l.replace(" ", "_")
                source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
                destination_folder = mm
                copy_images(source_folder, destination_folder)
create_folder_3_parts()
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In [5]:
#Create a folder for malignant seperation
def Create_Folder_Malignant():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_m/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='malignant']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
Create_Folder_Malignant()
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In [6]:
#Create a folder for 'benign' seperation
def Create_Folder_B():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_b/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='benign']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
            
 #Create a folder for non-neoplastic' seperation
def Create_Folder_N():
    parts = ['train','test','validation']
    for name in parts:
        m = 'C:/Users/dggua/Documents/DeepLearning/img_N/'+name
        os.mkdir(m)
        d = data.loc[data['three_partition_label']=='non-neoplastic']
        labels_unique = d['label'].unique()

        for l in labels_unique:
            l= l.replace(" ", "_")
            mm = m + '/'+ l
            os.mkdir(mm)
            source_folder = 'C:/Users/dggua/Documents/DeepLearning/img/'+ name + '/'+l
            destination_folder = mm
            copy_images(source_folder, destination_folder)
                       
Create_Folder_B()
Create_Folder_N()
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In [970]:
def Check_Number_SubFolders():
    print(len(df.label.unique()))
    print(df.three_partition_label.unique())
    print('------')
    for i in df.three_partition_label.unique():
        print(i)
        print(len(df.loc[df['three_partition_label']==i].label.unique()))
        print(len(df.loc[df['three_partition_label']==i]))
        print('....')
    print('------')
In [968]:
data['three_partition_label'].value_counts()
Out[968]:
three_partition_label
non-neoplastic    12045
malignant          2260
benign             2231
Name: count, dtype: int64
Split the dataset¶
In [914]:
def creating_folder_test_spit():
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img'
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
    #This is the directory where the images are stored 
    dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

    #This is the directory where the images will be stored after the split
    original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
    #Directories for the training, validation and test splits
    train_dir = os.path.join(original_dataset_dir, 'train')
     os.mkdir(train_dir)
    validation_dit = os.path.join(original_dataset_dir, 'validation')
     os.mkdir(validation_dit)
    test_dir = os.path.join(original_dataset_dir, 'test')
     os.mkdir(test_dir)

     #Create directories for each label in the training, validation and test splits
     for label in labels:
            train_label_dir = os.path.join(train_dir, label)
            os.mkdir(train_label_dir)
            validation_label_dir = os.path.join(validation_dit, label)
            os.mkdir(validation_label_dir)
            test_label_dir = os.path.join(test_dir, label)
            os.mkdir(test_label_dir)
            
        #Copy the images to the training, validation and test splits keeping the 60-20-20 ratio for each label with at least 53 images and a maximum of 653 images per

    for label in labels:
        label_dir = os.path.join(dw_dataset_dir, label)
        fnames = [f for f in os.listdir(label_dir) if f.endswith('.jpg')]
        np.random.shuffle(fnames)
        n = len(fnames)
        train_size = int(0.6*n)
        validation_size = int(0.2*n)
        test_size = n - train_size - validation_size
        train_fnames = fnames[:train_size]
        validation_fnames = fnames[train_size:train_size+validation_size]
        test_fnames = fnames[train_size+validation_size:]

        for fname in train_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(train_dir, label), fname)
            shutil.copyfile(src, dst)

        for fname in validation_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(validation_dit, label), fname)
            shutil.copyfile(src, dst)

        for fname in test_fnames:
            src = os.path.join(label_dir, fname)
            dst = os.path.join(os.path.join(test_dir, label), fname)
            shutil.copyfile(src, dst)

Step 2 Data preprocessing

  • Read the picture files.
  • Decode the JPEG content to RGB grids of pixels.
  • Convert these into floating-point tensors.
  • Rescale the pixel values (between 0 and 255) to the [0, 1] interval (as you know, neural networks prefer to deal with small input values).

Read the picture files and load each image file into an array. In which each element corresponds to a pixel with 3 channels with an integer from 0 to 255

Augment¶

In [5]:
def histogram_eq(img, bines,t):

    #count the number of pixels
    
    img = img
    
    img = img.astype(np.uint8)
    n = img.size
    print(n)
    #Get tje gary level histogram
    r = img.flatten() #0=black 255=white
    hist, bins = np.histogram(r, bines, [0,bines])
    Pf = hist/n

    #Get the cumulative distribution function
    cdf = np.cumsum(Pf)
    T = (bines-1)*cdf
    Trounding = np.round(T).astype('uint8')

    #Apply the transformation
    img_eq = Trounding[r].reshape(img.shape)

    return img_eq
In [6]:
def thresholding(f, L):
    f_tr = np.zeros(f.shape).astype('uint8')  # Initialize to zeros (background)
    f_tr[f <= L] = 255  
    return f_tr
In [7]:
#Otsu thresholding
def otsu_threshold(img):
    max_L = 256
    hist_t, bin_edges = np.histogram(img, bins=max_L, range=(0, max_L))
    M = np.product(img.shape)
    best_threshold = 0
    min_var = float('inf')

    for L in range(1, max_L - 1):
        w_a = np.sum(hist_t[:L]) / M
        w_b = np.sum(hist_t[L:]) / M
        sig_a = np.var(img[img < bin_edges[L]])
        sig_b = np.var(img[img >= bin_edges[L]])

        within_class_variance = w_a * sig_a + w_b * sig_b
        if within_class_variance < min_var:
            min_var = within_class_variance
            best_threshold = L

    img_t = thresholding(img, best_threshold)
    return img_t, best_threshold
In [8]:
def rgb_to_grayscale(rgb_values):
    rgb = rgb_values
    rgb = rgb.astype(np.uint8)
    rgb_img = Image.fromarray(rgb)
    gray = rgb_img.convert("L")
    return gray
In [9]:
from PIL import Image
def pipeline(X, label, name, m,num, t,n):
    #X = X.apply(pd.to_numeric, errors='coerce')
    if(t!='test'):
        for i in name:
            mm = m+'/' +i
            print(mm)
            files = os.listdir(mm)
            for j in files:
                num +=1
                image_path = mm+ '/'+j
                image = Image.open(image_path)
                q_image = histogram_eq(np.array(image), 256, t)
                qImage = Image.fromarray(q_image)
                qImage.save(image_path) 
                grayscale_image = rgb_to_grayscale(np.array(image))
                image_name = mm+'/'+ str(num) + '_g.jpg'
                grayscale_image.save(image_name) 
        
     
    else:
        for i in name:
            mm = m+'/' +i
            print(mm)
            files = os.listdir(mm)
            for j in files:
                image_path = mm+ '/'+j
                image = Image.open(image_path)
                q_image = histogram_eq(np.array(image), 256, t)
                qImage = Image.fromarray(q_image)
                qImage.save(image_path) 
    
    #plt.imshow(X)
    #return otsu_image, grayscale_image, eq_image, X
In [18]:
#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).
Found 1350 images belonging to 11 classes.
Found 462 images belonging to 11 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 11)
In [19]:
def create_images(generator,m, t):
    name =  os.listdir(m)
    n = generator.filenames
    count = 0
    c = 0
    if t == 'train':
        pipeline(0,0,name,m,count,t,n)
    else:
        pipeline(0,0,name,m,count,t,n)
        
create_images(train_generator,'C:/Users/dggua/Documents/DeepLearning/img_m/train', 'train')  
create_images(test_generator,'C:/Users/dggua/Documents/DeepLearning/img_m/test', 'test')  
C:/Users/dggua/Documents/DeepLearning/img_m/train/actinic_keratosis
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C:/Users/dggua/Documents/DeepLearning/img_m/test/squamous_cell_carcinoma
541458
481170
9256488
1225017
417774
343200
5781846
1747494
480000
2359296
382617
480000
577500
398580
698763
657624
7009038
529320
550164
531720
531987
551565
531900
385710
558207
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529620
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535194
530670
530334
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528957
529620
529074
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531000
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542361
529254
531525
530424
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531468
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529620
531525
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529620
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552240
542361
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530334
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357822
442650
502572
739845
308016
483756
385632
600600
480000
375480
414036
236775
183600
640284
717615
408975
334662
480000
531684
480000
393726
542544
794325
711204
480000
517032
619752
524970
480000
699720
730728
2359296
454410
168192
480000
11722752
1018368
3686400
2734236
520200
431877
480000
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1076355
411858
622434
C:/Users/dggua/Documents/DeepLearning/img_m/test/superficial_spreading_melanoma_ssm
1355940
546984
501840
433155
676962
386505
551565
418953
591138
358785
349860
383250
375945
712812
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475524
473634
395250
425064
1042440
393132
570261
354522
685764
499245
In [1860]:
 
Out[1860]:
array([ 0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  1,  1,  1,
        1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  2,  2,  2,  2,  2,
        2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  3,  3,  3,  3,  3,
        3,  3,  3,  3,  3,  3,  3,  4,  4,  4,  4,  4,  4,  4,  4,  4,  4,
        4,  4,  4,  4,  4,  4,  4,  4,  4,  5,  5,  5,  5,  5,  5,  5,  5,
        5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  5,  6,  6,  6,  6,  6,
        6,  6,  6,  6,  6,  6,  6,  6,  6,  6,  7,  7,  7,  7,  7,  7,  7,
        7,  7,  7,  7,  7,  7,  7,  7,  7,  7,  8,  8,  8,  8,  8,  8,  8,
        8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  8,  9,  9,  9,  9,
        9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,  9,
        9,  9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
       10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
       11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
       12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
       13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
       14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
       15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
       16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
       16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17,
       17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18,
       18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
       19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19,
       19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
       20, 20, 20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21,
       21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22,
       22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23,
       23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
       23, 23, 23, 23, 23, 23, 23, 23])
In [1671]:
def delete_images():
    directory = 'C:/Users/dggua/Documents/DeepLearning/img_3/train'

    # List the files in the directory
    files = os.listdir(directory)
    print(files)
    for i in files:
        directory2 = directory+"/"+i
        files2 = os.listdir(directory2)
        for j in files2:
            if ('img' in j):
                file_path = directory2+"/"+j
                os.remove(file_path)
In [ ]:
 

Generators¶

Color stretching¶

In [10]:
def channel_stretch(images):
    imagen_flotante = images.astype(np.float64)
    for canal in range(imagen_flotante.shape[2]):
        minimo = np.min(imagen_flotante[:,:,canal])
        maximo = np.max(imagen_flotante[:,:,canal])
        # Aplicar la transformación de estiramiento del contraste
        imagen_flotante[:,:,canal] = (imagen_flotante[:,:,canal] - minimo) / (maximo - minimo) * 255

    images_copy = imagen_flotante.astype(np.uint8)
    return images_copy
In [11]:
def batch_channel_stretch(batch_images):
    # Convert to float to avoid issues with integer overflow/underflow
    batch_images_float = batch_images.astype(np.float64)
    
    for i in range(batch_images_float.shape[0]):  # Iterate over each image in the batch
        for channel in range(batch_images_float.shape[-1]):  # Iterate over each channel
            # Calculate min and max values for the current channel of the current image
            min_val = np.min(batch_images_float[i, :, :, channel])
            max_val = np.max(batch_images_float[i, :, :, channel])
            # Avoid division by zero if the image is constant
            if max_val > min_val:
                # Normalize the current channel of the current image
                batch_images_float[i, :, :, channel] = (batch_images_float[i, :, :, channel] - min_val) / (max_val - min_val) * 255
            else:
                # If max and min are the same, set the channel to zeros (or you might choose 255 for a white image)
                batch_images_float[i, :, :, channel] = np.zeros_like(batch_images_float[i, :, :, channel])
    
    # Convert back to unsigned 8-bit integer type
    return batch_images_float.astype(np.uint8)
In [12]:
img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

imagen_final = channel_stretch(img2)

plt.figure(figsize=(20,10))
plt.subplot(131); plt.imshow(img2)
plt.subplot(132); plt.imshow(imagen_final)
plt.show()
C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\3812641245.py:1: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')
In [13]:
## Pre-trained Model VGG16
!pip install keras.applications.vgg16
ERROR: Could not find a version that satisfies the requirement keras.applications.vgg16 (from versions: none)
ERROR: No matching distribution found for keras.applications.vgg16

Color Descriptors¶

In [14]:
img1 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/dariers_disease/img145.jpg')
img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')

plt.figure(figsize=(20,10))
plt.subplot(131) ; plt.imshow(img1[:,:,0], cmap='gray') ; plt.title('RED')
plt.subplot(132) ; plt.imshow(img1[:,:,1], cmap='gray') ; plt.title('GREEN')
plt.subplot(133) ; plt.imshow(img1[:,:,2], cmap='gray') ; plt.title('BLUE')
C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\57107206.py:1: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img1 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/dariers_disease/img145.jpg')
C:\Users\dggua\AppData\Local\Temp\ipykernel_1528\57107206.py:2: DeprecationWarning: Starting with ImageIO v3 the behavior of this function will switch to that of iio.v3.imread. To keep the current behavior (and make this warning disappear) use `import imageio.v2 as imageio` or call `imageio.v2.imread` directly.
  img2 = imageio.imread('C:/Users/dggua/Documents/DeepLearning/imgPrueba/melanoma/img1528.jpg')
Out[14]:
Text(0.5, 1.0, 'BLUE')

Color Stretching Examples¶

In [15]:
train_images, train_labels = next(train_generator)
validation_images, validation_labels = next(validation_generator)

train_images_stretched = list(map(channel_stretch,train_images))
validation_images_stretched = channel_stretch(validation_images)


plt.figure(figsize=(15,10))
plt.subplot(131); plt.imshow(train_images[10])
plt.subplot(132); plt.imshow(train_images_stretched[10])
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[15], line 2
      1 train_images, train_labels = next(train_generator)
----> 2 validation_images, validation_labels = next(validation_generator)
      4 train_images_stretched = list(map(channel_stretch,train_images))
      5 validation_images_stretched = channel_stretch(validation_images)

NameError: name 'validation_generator' is not defined

Feature Extraction¶

Step 3 Building the network

In [20]:
def recall_m(y_true, y_pred):
    true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
    possible_positives = K.sum(K.round(K.clip(y_true, 0, 1)))
    recall = true_positives / (possible_positives + K.epsilon())
    return recall

def precision_m(y_true, y_pred):
    true_positives = K.sum(K.round(K.clip(y_true * y_pred, 0, 1)))
    predicted_positives = K.sum(K.round(K.clip(y_pred, 0, 1)))

    precision = true_positives / (predicted_positives + K.epsilon())
    return precision

def f1_m(y_true, y_pred):
    precision = precision_m(y_true, y_pred)
    recall = recall_m(y_true, y_pred)
    return 2*((precision*recall)/(precision+recall+K.epsilon()))

def f1_weighted(true, pred): #shapes (batch, 4)

    #for metrics include these two lines, for loss, don't include them
    #these are meant to round 'pred' to exactly zeros and ones
    #predLabels = K.argmax(pred, axis=-1)
    #pred = K.one_hot(predLabels, 4) 


    ground_positives = K.sum(true, axis=0) + K.epsilon()       # = TP + FN
    pred_positives = K.sum(pred, axis=0) + K.epsilon()         # = TP + FP
    true_positives = K.sum(true * pred, axis=0) + K.epsilon()  # = TP
        #all with shape (4,)
    
    precision = true_positives / pred_positives 
    recall = true_positives / ground_positives
        #both = 1 if ground_positives == 0 or pred_positives == 0
        #shape (4,)

    f1 = 2 * (precision * recall) / (precision + recall + K.epsilon())
        #still with shape (4,)

    weighted_f1 = f1 * ground_positives / K.sum(ground_positives) 
    weighted_f1 = K.sum(weighted_f1)

    
    return 1 - weighted_f1
In [21]:
#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).
Found 19730 images belonging to 3 classes.
Found 3260 images belonging to 3 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 3)
In [22]:
IMG_SIZE = 200

resize_and_rescale = Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
data_augmentation = Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\backend.py:873: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

In [ ]:

In [23]:
IMG_SIZE = 200
model = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(50, 50, 3)))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(64, (3, 3), activation='relu'))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Conv2D(128, (3, 3), activation='relu'))
model.add(layers.MaxPooling2D((2, 2)))
model.add(layers.Flatten())
model.add(layers.Dropout(0.5))
model.add(layers.Dense(512, activation='relu'))
model.add(layers.Dense(3, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])
WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\layers\pooling\max_pooling2d.py:161: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.

WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.
In [24]:
history = model.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=10,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model.save('Dermatology_problem_v1.h5')
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\1661183745.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history = model.fit_generator(
Epoch 1/10
WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\utils\tf_utils.py:492: The name tf.ragged.RaggedTensorValue is deprecated. Please use tf.compat.v1.ragged.RaggedTensorValue instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\utils\tf_utils.py:492: The name tf.ragged.RaggedTensorValue is deprecated. Please use tf.compat.v1.ragged.RaggedTensorValue instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\base_layer_utils.py:384: The name tf.executing_eagerly_outside_functions is deprecated. Please use tf.compat.v1.executing_eagerly_outside_functions instead.

WARNING:tensorflow:From C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\base_layer_utils.py:384: The name tf.executing_eagerly_outside_functions is deprecated. Please use tf.compat.v1.executing_eagerly_outside_functions instead.

154/154 [==============================] - 1686s 11s/step - loss: 1.0476 - accuracy: 0.7206 - precision: 0.7291 - recall: 0.6933 - f1_m: 0.6930 - f1_weighted: 0.4464 - val_loss: 0.7669 - val_accuracy: 0.7303 - val_precision: 0.7303 - val_recall: 0.7303 - val_f1_m: 0.7303 - val_f1_weighted: 0.4336
Epoch 2/10
154/154 [==============================] - 1450s 9s/step - loss: 0.7674 - accuracy: 0.7288 - precision: 0.7330 - recall: 0.7219 - f1_m: 0.7263 - f1_weighted: 0.4269 - val_loss: 0.7551 - val_accuracy: 0.7275 - val_precision: 0.7284 - val_recall: 0.7275 - val_f1_m: 0.7280 - val_f1_weighted: 0.4268
Epoch 3/10
154/154 [==============================] - 1453s 9s/step - loss: 0.7585 - accuracy: 0.7298 - precision: 0.7362 - recall: 0.7193 - f1_m: 0.7260 - f1_weighted: 0.4234 - val_loss: 0.7542 - val_accuracy: 0.7284 - val_precision: 0.7303 - val_recall: 0.7278 - val_f1_m: 0.7290 - val_f1_weighted: 0.4153
Epoch 4/10
154/154 [==============================] - 1471s 10s/step - loss: 0.7514 - accuracy: 0.7293 - precision: 0.7370 - recall: 0.7178 - f1_m: 0.7272 - f1_weighted: 0.4182 - val_loss: 0.7560 - val_accuracy: 0.7334 - val_precision: 0.7440 - val_recall: 0.7138 - val_f1_m: 0.7285 - val_f1_weighted: 0.4379
Epoch 5/10
154/154 [==============================] - 1449s 9s/step - loss: 0.7493 - accuracy: 0.7306 - precision: 0.7395 - recall: 0.7166 - f1_m: 0.7266 - f1_weighted: 0.4172 - val_loss: 0.7449 - val_accuracy: 0.7309 - val_precision: 0.7330 - val_recall: 0.7250 - val_f1_m: 0.7289 - val_f1_weighted: 0.4229
Epoch 6/10
154/154 [==============================] - 1462s 9s/step - loss: 0.7439 - accuracy: 0.7315 - precision: 0.7422 - recall: 0.7124 - f1_m: 0.7269 - f1_weighted: 0.4140 - val_loss: 0.7411 - val_accuracy: 0.7294 - val_precision: 0.7419 - val_recall: 0.7169 - val_f1_m: 0.7291 - val_f1_weighted: 0.4247
Epoch 7/10
154/154 [==============================] - 1442s 9s/step - loss: 0.7388 - accuracy: 0.7340 - precision: 0.7451 - recall: 0.7148 - f1_m: 0.7290 - f1_weighted: 0.4113 - val_loss: 0.7286 - val_accuracy: 0.7344 - val_precision: 0.7441 - val_recall: 0.7241 - val_f1_m: 0.7339 - val_f1_weighted: 0.4047
Epoch 8/10
154/154 [==============================] - 1450s 9s/step - loss: 0.7341 - accuracy: 0.7340 - precision: 0.7471 - recall: 0.7131 - f1_m: 0.7294 - f1_weighted: 0.4087 - val_loss: 0.7335 - val_accuracy: 0.7366 - val_precision: 0.7433 - val_recall: 0.7247 - val_f1_m: 0.7339 - val_f1_weighted: 0.3971
Epoch 9/10
154/154 [==============================] - 1446s 9s/step - loss: 0.7281 - accuracy: 0.7356 - precision: 0.7492 - recall: 0.7135 - f1_m: 0.7293 - f1_weighted: 0.4063 - val_loss: 0.7405 - val_accuracy: 0.7297 - val_precision: 0.7363 - val_recall: 0.7278 - val_f1_m: 0.7320 - val_f1_weighted: 0.3995
Epoch 10/10
154/154 [==============================] - 1439s 9s/step - loss: 0.7280 - accuracy: 0.7354 - precision: 0.7506 - recall: 0.7116 - f1_m: 0.7301 - f1_weighted: 0.4043 - val_loss: 0.7354 - val_accuracy: 0.7372 - val_precision: 0.7464 - val_recall: 0.7212 - val_f1_m: 0.7337 - val_f1_weighted: 0.3893
C:\Users\dggua\anaconda3\Lib\site-packages\keras\src\engine\training.py:3103: UserWarning: You are saving your model as an HDF5 file via `model.save()`. This file format is considered legacy. We recommend using instead the native Keras format, e.g. `model.save('my_model.keras')`.
  saving_api.save_model(

Step 3 Model Fitting

Identify corrupted image files¶
In [146]:
def delete_corrpted_images():
#Images corrupted image files, unsupported image formats, or incorrect file paths 

 for label in labels:
    label_dir = os.path.join(validation_dit, label)
    for fname in os.listdir(label_dir):
        try:
            img = cv2.imread(os.path.join(label_dir, fname))
            if img is None:
                print('File {} is not a valid image file'.format(fname), label)
        except:
            print('File {} is not a valid image file'.format(fname), label)
In [429]:
#tf.keras.backend.clear_session()
In [ ]:
 
In [ ]:
 

Step 4 Plot metrics

In [980]:
def Plot_Metrics():
    #Now we will plot the training and validation accuracy and loss
    metric = 'accuracy' #sensitivity, specificity, precision, recall, f1-score can also be used
    acc = history.history[metric]
    val_acc = history.history['val_accuracy']
    loss = history.history['loss']
    val_loss = history.history['val_loss']

    epochs = range(1, len(acc) + 1)

    plt.plot(epochs, acc, 'bo', label='Training acc')
    plt.plot(epochs, val_acc, 'b', label='Validation acc')
    plt.title('Training and validation accuracy')
    plt.legend()

    plt.figure()

    plt.plot(epochs, loss, 'bo', label='Training loss')
    plt.plot(epochs, val_loss, 'b', label='Validation loss')
    plt.title('Training and validation loss')
    plt.legend()

    plt.show()
    print(test_datagen)
    #Now we will evaluate the model on the test set
    #test_loss, test_acc = model.evaluate_generator(test_datagen, steps=50)
    #print('test acc:', test_acc)

    #Now we will make predictions on the test set
    predictions = model.predict_generator(validation_generator, steps=50)
    print(predictions)

Run the first Model to check the results¶

In [1]:
#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).
---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Cell In[1], line 4
      2 original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'
      3 #Directories for the training, validation and test splits
----> 4 train_dir = os.path.join(original_dataset_dir, 'train')
      5 # os.mkdir(train_dir)
      6 validation_dit = os.path.join(original_dataset_dir, 'validation')

NameError: name 'os' is not defined
In [1374]:
#Creating Predictions
predictions = model.predict_generator(test_generator,  verbose = 1)
C:\Users\dggua\AppData\Local\Temp\ipykernel_10776\846870615.py:2: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions = model.predict_generator(test_generator,  verbose = 1)
27/27 [==============================] - 188s 7s/step
In [1377]:
predictions[0]
Out[1377]:
array([0.18996486, 0.59574866, 0.21428649], dtype=float32)
In [1378]:
#Checking how many rights and wrongs prediction we got
points = 0
points_w = 0
c = 0
class_indices = train_generator.classes
at = []
for i in predictions: 
    random_num = round(random.uniform(0, 1), 8)
    classi = 0
    if(random_num <= i[0]):
        classi = 0
    elif((random_num > i[0]) and (random_num<=(i[1]+i[0]))):
        classi = 1
    else:
        classi = 2
    if(classi==class_indices[c]):
        points+=1
        at.append(classi)
    else:
        points_w+=1
        at.append(4)
    c+=1

print(points, points_w)
print(points/(points+points_w))
print(Counter(at))
print(Counter(class_indices))
849 2552
0.24963246104087033
Counter({4: 2552, 1: 502, 0: 347})
Counter({1: 14374, 0: 2700, 2: 2656})

Run the Models for belign, Malignant and non-neoplastic¶

take in mind if there is a problem please run:¶
#### tf.keras.backend.clear_session()
In [1908]:
tf.keras.backend.clear_session()
In [25]:
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)
In [26]:
#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break

#El generador produce lotes de imágenes de tamaño 150x150 (altura y ancho) y 3 (canales de color) y lotes de etiquetas de tamaño 30 (número de imágenes en el lote).
Found 2656 images belonging to 24 classes.
Found 436 images belonging to 24 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 24)
In [27]:
train_generator.class_indices.keys()
Out[27]:
dict_keys(['becker_nevus', 'congenital_nevus', 'dermatofibroma', 'disseminated_actinic_porokeratosis', 'epidermal_nevus', 'fordyce_spots', 'granuloma_pyogenic', 'halo_nevus', 'lymphangioma', 'milia', 'mucous_cyst', 'naevus_comedonicus', 'nevocytic_nevus', 'nevus_sebaceous_of_jadassohn', 'pilar_cyst', 'pilomatricoma', 'porokeratosis_actinic', 'porokeratosis_of_mibelli', 'port_wine_stain', 'prurigo_nodularis', 'pyogenic_granuloma', 'seborrheic_keratosis', 'syringoma', 'telangiectases'])
In [28]:
IMG_SIZE = 200
model2 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model2 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model2.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(64, (3, 3), activation='relu'))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Conv2D(128, (3, 3), activation='relu'))
model2.add(layers.MaxPooling2D((2, 2)))
model2.add(layers.Flatten())
model2.add(layers.Dropout(0.5))
model2.add(layers.Dense(512, activation='relu'))
model2.add(layers.Dense(24, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model2.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])
WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.
In [ ]:
 
In [29]:
history = model2.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=20,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model2.save('Dermatology_problem_v1_b.h5')
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\2294588897.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history = model2.fit_generator(
Epoch 1/20
20/20 [==============================] - 224s 11s/step - loss: 3.6800 - accuracy: 0.0653 - precision: 0.0547 - recall: 0.0028 - f1_m: 0.0027 - f1_weighted: 0.9557 - val_loss: 3.1281 - val_accuracy: 0.0703 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9527
Epoch 2/20
20/20 [==============================] - 190s 9s/step - loss: 3.1418 - accuracy: 0.0783 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9521 - val_loss: 3.1317 - val_accuracy: 0.0703 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9527
Epoch 3/20
20/20 [==============================] - 184s 9s/step - loss: 3.1360 - accuracy: 0.0803 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9516 - val_loss: 3.1112 - val_accuracy: 0.0755 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9515
Epoch 4/20
20/20 [==============================] - 183s 9s/step - loss: 3.1162 - accuracy: 0.0866 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9495 - val_loss: 3.1213 - val_accuracy: 0.0729 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9515
Epoch 5/20
20/20 [==============================] - 183s 9s/step - loss: 3.1183 - accuracy: 0.0878 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9498 - val_loss: 3.0969 - val_accuracy: 0.0911 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9506
Epoch 6/20
20/20 [==============================] - 183s 9s/step - loss: 3.1115 - accuracy: 0.0996 - precision: 0.2857 - recall: 7.8125e-04 - f1_m: 0.0015 - f1_weighted: 0.9486 - val_loss: 3.0758 - val_accuracy: 0.0911 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9496
Epoch 7/20
20/20 [==============================] - 201s 10s/step - loss: 3.0673 - accuracy: 0.1036 - precision: 0.2000 - recall: 3.9557e-04 - f1_m: 7.5758e-04 - f1_weighted: 0.9452 - val_loss: 4.4223 - val_accuracy: 0.0234 - val_precision: 0.0427 - val_recall: 0.0234 - val_f1_m: 0.0305 - val_f1_weighted: 0.9730
Epoch 8/20
20/20 [==============================] - 330s 16s/step - loss: 3.1310 - accuracy: 0.0989 - precision: 0.0769 - recall: 0.0016 - f1_m: 0.0025 - f1_weighted: 0.9459 - val_loss: 3.0750 - val_accuracy: 0.0885 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9474
Epoch 9/20
20/20 [==============================] - 184s 9s/step - loss: 3.0497 - accuracy: 0.1112 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9413 - val_loss: 3.0215 - val_accuracy: 0.1406 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9449
Epoch 10/20
20/20 [==============================] - 184s 9s/step - loss: 3.0020 - accuracy: 0.1353 - precision: 0.3125 - recall: 0.0020 - f1_m: 0.0035 - f1_weighted: 0.9374 - val_loss: 2.9877 - val_accuracy: 0.1250 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9400
Epoch 11/20
20/20 [==============================] - 184s 9s/step - loss: 2.9799 - accuracy: 0.1218 - precision: 0.1667 - recall: 0.0012 - f1_m: 0.0022 - f1_weighted: 0.9348 - val_loss: 3.0206 - val_accuracy: 0.1146 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9388
Epoch 12/20
20/20 [==============================] - 182s 9s/step - loss: 2.9826 - accuracy: 0.1262 - precision: 0.6667 - recall: 0.0040 - f1_m: 0.0077 - f1_weighted: 0.9345 - val_loss: 2.9905 - val_accuracy: 0.1172 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9385
Epoch 13/20
20/20 [==============================] - 184s 9s/step - loss: 2.9474 - accuracy: 0.1499 - precision: 0.3333 - recall: 0.0028 - f1_m: 0.0052 - f1_weighted: 0.9303 - val_loss: 2.9537 - val_accuracy: 0.1276 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9370
Epoch 14/20
20/20 [==============================] - 182s 9s/step - loss: 2.9267 - accuracy: 0.1420 - precision: 0.4167 - recall: 0.0020 - f1_m: 0.0038 - f1_weighted: 0.9284 - val_loss: 2.9504 - val_accuracy: 0.1458 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9379
Epoch 15/20
20/20 [==============================] - 183s 9s/step - loss: 2.9132 - accuracy: 0.1602 - precision: 0.2500 - recall: 0.0036 - f1_m: 0.0067 - f1_weighted: 0.9246 - val_loss: 2.9760 - val_accuracy: 0.1172 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9357
Epoch 16/20
20/20 [==============================] - 183s 9s/step - loss: 2.8798 - accuracy: 0.1594 - precision: 0.4324 - recall: 0.0063 - f1_m: 0.0121 - f1_weighted: 0.9208 - val_loss: 2.9440 - val_accuracy: 0.1224 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9355
Epoch 17/20
20/20 [==============================] - 186s 9s/step - loss: 2.8666 - accuracy: 0.1638 - precision: 0.3750 - recall: 0.0036 - f1_m: 0.0069 - f1_weighted: 0.9201 - val_loss: 2.8910 - val_accuracy: 0.1771 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9238
Epoch 18/20
20/20 [==============================] - 183s 9s/step - loss: 2.8467 - accuracy: 0.1776 - precision: 0.4423 - recall: 0.0091 - f1_m: 0.0175 - f1_weighted: 0.9155 - val_loss: 2.9009 - val_accuracy: 0.1510 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9281
Epoch 19/20
20/20 [==============================] - 183s 9s/step - loss: 2.8216 - accuracy: 0.1764 - precision: 0.3750 - recall: 0.0071 - f1_m: 0.0137 - f1_weighted: 0.9127 - val_loss: 2.8941 - val_accuracy: 0.1432 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9285
Epoch 20/20
20/20 [==============================] - 182s 9s/step - loss: 2.8047 - accuracy: 0.1784 - precision: 0.4500 - recall: 0.0142 - f1_m: 0.0271 - f1_weighted: 0.9098 - val_loss: 2.8531 - val_accuracy: 0.1615 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9234
In [31]:
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)
In [32]:
train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break
Found 14374 images belonging to 79 classes.
Found 2376 images belonging to 79 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 79)
In [33]:
IMG_SIZE = 200
model3 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model3 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model3.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(64, (3, 3), activation='relu'))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Conv2D(128, (3, 3), activation='relu'))
model3.add(layers.MaxPooling2D((2, 2)))
model3.add(layers.Flatten())
model3.add(layers.Dropout(0.5))
model3.add(layers.Dense(512, activation='relu'))
model3.add(layers.Dense(79, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model3.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])
WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.
In [34]:
history3 = model3.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=15,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model3.save('Dermatology_problem_v1_n.h5')
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\494932761.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history3 = model3.fit_generator(
Epoch 1/15
112/112 [==============================] - 1212s 11s/step - loss: 4.2005 - accuracy: 0.0523 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9790 - val_loss: 4.1395 - val_accuracy: 0.0556 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9775
Epoch 2/15
112/112 [==============================] - 1034s 9s/step - loss: 4.1505 - accuracy: 0.0543 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9782 - val_loss: 4.1668 - val_accuracy: 0.0556 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9797
Epoch 3/15
112/112 [==============================] - 1027s 9s/step - loss: 4.1361 - accuracy: 0.0537 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9777 - val_loss: 4.1181 - val_accuracy: 0.0516 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9778
Epoch 4/15
112/112 [==============================] - 1024s 9s/step - loss: 4.0842 - accuracy: 0.0597 - precision: 0.0000e+00 - recall: 0.0000e+00 - f1_m: 0.0000e+00 - f1_weighted: 0.9756 - val_loss: 4.0504 - val_accuracy: 0.0551 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9738
Epoch 5/15
112/112 [==============================] - 1136s 10s/step - loss: 4.0385 - accuracy: 0.0623 - precision: 0.1429 - recall: 7.0195e-05 - f1_m: 1.3843e-04 - f1_weighted: 0.9734 - val_loss: 4.0665 - val_accuracy: 0.0499 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9746
Epoch 6/15
112/112 [==============================] - 1054s 9s/step - loss: 3.9974 - accuracy: 0.0691 - precision: 0.1250 - recall: 7.0195e-05 - f1_m: 1.3736e-04 - f1_weighted: 0.9717 - val_loss: 3.9897 - val_accuracy: 0.0681 - val_precision: 0.5000 - val_recall: 8.6806e-04 - val_f1_m: 0.0017 - val_f1_weighted: 0.9680
Epoch 7/15
112/112 [==============================] - 1053s 9s/step - loss: 3.9618 - accuracy: 0.0737 - precision: 0.5385 - recall: 9.8273e-04 - f1_m: 0.0019 - f1_weighted: 0.9692 - val_loss: 3.9465 - val_accuracy: 0.0642 - val_precision: 0.3784 - val_recall: 0.0061 - val_f1_m: 0.0118 - val_f1_weighted: 0.9662
Epoch 8/15
112/112 [==============================] - 1230s 11s/step - loss: 3.9167 - accuracy: 0.0817 - precision: 0.5439 - recall: 0.0022 - f1_m: 0.0043 - f1_weighted: 0.9664 - val_loss: 3.9646 - val_accuracy: 0.0738 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.9704
Epoch 9/15
112/112 [==============================] - 1052s 9s/step - loss: 3.8753 - accuracy: 0.0833 - precision: 0.5781 - recall: 0.0026 - f1_m: 0.0051 - f1_weighted: 0.9637 - val_loss: 3.8977 - val_accuracy: 0.0890 - val_precision: 0.5833 - val_recall: 0.0030 - val_f1_m: 0.0060 - val_f1_weighted: 0.9633
Epoch 10/15
112/112 [==============================] - 1063s 9s/step - loss: 3.8242 - accuracy: 0.0940 - precision: 0.6042 - recall: 0.0041 - f1_m: 0.0079 - f1_weighted: 0.9604 - val_loss: 3.8554 - val_accuracy: 0.0872 - val_precision: 0.4615 - val_recall: 0.0052 - val_f1_m: 0.0103 - val_f1_weighted: 0.9610
Epoch 11/15
112/112 [==============================] - 1092s 10s/step - loss: 3.7782 - accuracy: 0.0997 - precision: 0.5250 - recall: 0.0044 - f1_m: 0.0086 - f1_weighted: 0.9571 - val_loss: 3.9315 - val_accuracy: 0.0877 - val_precision: 0.6154 - val_recall: 0.0035 - val_f1_m: 0.0069 - val_f1_weighted: 0.9575
Epoch 12/15
112/112 [==============================] - 1057s 9s/step - loss: 3.7343 - accuracy: 0.1061 - precision: 0.6567 - recall: 0.0062 - f1_m: 0.0121 - f1_weighted: 0.9534 - val_loss: 3.7813 - val_accuracy: 0.1072 - val_precision: 0.5143 - val_recall: 0.0078 - val_f1_m: 0.0153 - val_f1_weighted: 0.9524
Epoch 13/15
112/112 [==============================] - 1056s 9s/step - loss: 3.6911 - accuracy: 0.1135 - precision: 0.6183 - recall: 0.0081 - f1_m: 0.0160 - f1_weighted: 0.9498 - val_loss: 3.8485 - val_accuracy: 0.0972 - val_precision: 0.5789 - val_recall: 0.0095 - val_f1_m: 0.0186 - val_f1_weighted: 0.9514
Epoch 14/15
112/112 [==============================] - 1057s 9s/step - loss: 3.6539 - accuracy: 0.1233 - precision: 0.5917 - recall: 0.0070 - f1_m: 0.0143 - f1_weighted: 0.9465 - val_loss: 3.7569 - val_accuracy: 0.1146 - val_precision: 0.5490 - val_recall: 0.0122 - val_f1_m: 0.0236 - val_f1_weighted: 0.9480
Epoch 15/15
112/112 [==============================] - 1052s 9s/step - loss: 3.6154 - accuracy: 0.1249 - precision: 0.6540 - recall: 0.0097 - f1_m: 0.0191 - f1_weighted: 0.9431 - val_loss: 3.7614 - val_accuracy: 0.0951 - val_precision: 0.7000 - val_recall: 0.0091 - val_f1_m: 0.0179 - val_f1_weighted: 0.9485
In [35]:
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits
train_dir = os.path.join(original_dataset_dir, 'train')
# os.mkdir(train_dir)
validation_dit = os.path.join(original_dataset_dir, 'validation')
# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)
    
In [36]:
train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )
test_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True)

# Now, use flow_from_directory without specifying preprocessing_function again

train_generator = train_datagen.flow_from_directory(
    train_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)

    
validation_generator = test_datagen.flow_from_directory(
    validation_dit,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)

print(type(train_generator))
for data_batch, labels_batch in train_generator:
    print('data batch shape:', data_batch.shape)
    print('labels batch shape:', labels_batch.shape)
    break
Found 2700 images belonging to 11 classes.
Found 448 images belonging to 11 classes.
<class 'keras.src.preprocessing.image.DirectoryIterator'>
data batch shape: (128, 200, 200, 3)
labels batch shape: (128, 11)
In [37]:
IMG_SIZE = 200
model4 = models.Sequential([
  layers.Resizing(IMG_SIZE, IMG_SIZE),
  layers.Rescaling(1./255)
])
model4 = models.Sequential([
  layers.RandomFlip("horizontal_and_vertical"),
  layers.RandomRotation(0.4),
])
model4.add(layers.Conv2D(32, (3, 3), activation='relu', input_shape=(200, 200, 3)))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(64, (3, 3), activation='relu'))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(128, (3, 3), activation='relu'))
    #model.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Conv2D(128, (3, 3), activation='relu'))
model4.add(layers.MaxPooling2D((2, 2)))
model4.add(layers.Flatten())
model4.add(layers.Dropout(0.5))
model4.add(layers.Dense(512, activation='relu'))
model4.add(layers.Dense(11, activation='softmax'))  # Output layer with 114 units and sigmoid activation

model4.compile(optimizer=optimizers.RMSprop(lr=1e-4),
                  loss='categorical_crossentropy',
                  metrics=['accuracy','Precision','Recall',f1_m,f1_weighted])
WARNING:absl:`lr` is deprecated in Keras optimizer, please use `learning_rate` or use the legacy optimizer, e.g.,tf.keras.optimizers.legacy.RMSprop.
In [38]:
history4 = model4.fit_generator(
    train_generator,
    steps_per_epoch=train_generator.n//train_generator.batch_size,
    epochs=20,
    validation_data=validation_generator,
    validation_steps=validation_generator.n//validation_generator.batch_size
)

model4.save('Dermatology_problem_v1_m.h5')
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\1713391298.py:1: UserWarning: `Model.fit_generator` is deprecated and will be removed in a future version. Please use `Model.fit`, which supports generators.
  history4 = model4.fit_generator(
Epoch 1/20
21/21 [==============================] - 229s 11s/step - loss: 3.7929 - accuracy: 0.2274 - precision: 0.2081 - recall: 0.0358 - f1_m: 0.0368 - f1_weighted: 0.8699 - val_loss: 2.1746 - val_accuracy: 0.2422 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8589
Epoch 2/20
21/21 [==============================] - 193s 9s/step - loss: 2.1946 - accuracy: 0.2508 - precision: 0.4091 - recall: 0.0035 - f1_m: 0.0059 - f1_weighted: 0.8556 - val_loss: 2.1445 - val_accuracy: 0.2083 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8585
Epoch 3/20
21/21 [==============================] - 193s 9s/step - loss: 2.1625 - accuracy: 0.2481 - precision: 0.1250 - recall: 3.8880e-04 - f1_m: 7.0028e-04 - f1_weighted: 0.8553 - val_loss: 2.1522 - val_accuracy: 0.2474 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8613
Epoch 4/20
21/21 [==============================] - 190s 9s/step - loss: 2.1909 - accuracy: 0.2216 - precision: 0.2479 - recall: 0.0117 - f1_m: 0.0125 - f1_weighted: 0.8580 - val_loss: 2.1202 - val_accuracy: 0.2630 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8486
Epoch 5/20
21/21 [==============================] - 189s 9s/step - loss: 2.1546 - accuracy: 0.2597 - precision: 0.4000 - recall: 0.0016 - f1_m: 0.0028 - f1_weighted: 0.8558 - val_loss: 2.1310 - val_accuracy: 0.2500 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8453
Epoch 6/20
21/21 [==============================] - 197s 9s/step - loss: 2.1397 - accuracy: 0.2507 - precision: 0.6667 - recall: 7.4405e-04 - f1_m: 0.0015 - f1_weighted: 0.8512 - val_loss: 2.1384 - val_accuracy: 0.2292 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8433
Epoch 7/20
21/21 [==============================] - 189s 9s/step - loss: 2.1345 - accuracy: 0.2714 - precision: 0.3514 - recall: 0.0051 - f1_m: 0.0081 - f1_weighted: 0.8508 - val_loss: 2.2374 - val_accuracy: 0.2552 - val_precision: 0.3750 - val_recall: 0.0469 - val_f1_m: 0.0827 - val_f1_weighted: 0.8439
Epoch 8/20
21/21 [==============================] - 193s 9s/step - loss: 2.1184 - accuracy: 0.2562 - precision: 0.4348 - recall: 0.0039 - f1_m: 0.0070 - f1_weighted: 0.8464 - val_loss: 2.0953 - val_accuracy: 0.2760 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8482
Epoch 9/20
21/21 [==============================] - 189s 9s/step - loss: 2.0796 - accuracy: 0.2788 - precision: 0.4058 - recall: 0.0109 - f1_m: 0.0209 - f1_weighted: 0.8404 - val_loss: 2.1454 - val_accuracy: 0.2500 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8437
Epoch 10/20
21/21 [==============================] - 189s 9s/step - loss: 2.0736 - accuracy: 0.2807 - precision: 0.4286 - recall: 0.0035 - f1_m: 0.0065 - f1_weighted: 0.8401 - val_loss: 2.1259 - val_accuracy: 0.2708 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8567
Epoch 11/20
21/21 [==============================] - 189s 9s/step - loss: 2.0364 - accuracy: 0.2885 - precision: 0.4583 - recall: 0.0086 - f1_m: 0.0146 - f1_weighted: 0.8300 - val_loss: 2.0777 - val_accuracy: 0.2969 - val_precision: 0.5455 - val_recall: 0.0156 - val_f1_m: 0.0300 - val_f1_weighted: 0.8296
Epoch 12/20
21/21 [==============================] - 191s 9s/step - loss: 2.0524 - accuracy: 0.2846 - precision: 0.4500 - recall: 0.0140 - f1_m: 0.0253 - f1_weighted: 0.8271 - val_loss: 2.0783 - val_accuracy: 0.2708 - val_precision: 0.0000e+00 - val_recall: 0.0000e+00 - val_f1_m: 0.0000e+00 - val_f1_weighted: 0.8405
Epoch 13/20
21/21 [==============================] - 187s 9s/step - loss: 2.0020 - accuracy: 0.2951 - precision: 0.5714 - recall: 0.0156 - f1_m: 0.0277 - f1_weighted: 0.8220 - val_loss: 2.0173 - val_accuracy: 0.2682 - val_precision: 0.3750 - val_recall: 0.0078 - val_f1_m: 0.0152 - val_f1_weighted: 0.8241
Epoch 14/20
21/21 [==============================] - 187s 9s/step - loss: 1.9808 - accuracy: 0.3075 - precision: 0.5051 - recall: 0.0194 - f1_m: 0.0402 - f1_weighted: 0.8155 - val_loss: 1.9918 - val_accuracy: 0.2969 - val_precision: 0.7333 - val_recall: 0.0286 - val_f1_m: 0.0547 - val_f1_weighted: 0.8104
Epoch 15/20
21/21 [==============================] - 195s 9s/step - loss: 1.9799 - accuracy: 0.3058 - precision: 0.4936 - recall: 0.0286 - f1_m: 0.0522 - f1_weighted: 0.8137 - val_loss: 1.9550 - val_accuracy: 0.2969 - val_precision: 0.7143 - val_recall: 0.0130 - val_f1_m: 0.0255 - val_f1_weighted: 0.8158
Epoch 16/20
21/21 [==============================] - 188s 9s/step - loss: 1.9697 - accuracy: 0.3103 - precision: 0.5247 - recall: 0.0330 - f1_m: 0.0630 - f1_weighted: 0.8100 - val_loss: 2.0683 - val_accuracy: 0.2734 - val_precision: 0.5333 - val_recall: 0.0208 - val_f1_m: 0.0400 - val_f1_weighted: 0.8325
Epoch 17/20
21/21 [==============================] - 188s 9s/step - loss: 1.9745 - accuracy: 0.3184 - precision: 0.4505 - recall: 0.0389 - f1_m: 0.0647 - f1_weighted: 0.8048 - val_loss: 1.9751 - val_accuracy: 0.2708 - val_precision: 0.5238 - val_recall: 0.0286 - val_f1_m: 0.0544 - val_f1_weighted: 0.8141
Epoch 18/20
21/21 [==============================] - 191s 9s/step - loss: 1.9497 - accuracy: 0.3157 - precision: 0.5176 - recall: 0.0342 - f1_m: 0.0666 - f1_weighted: 0.8053 - val_loss: 1.9916 - val_accuracy: 0.3073 - val_precision: 0.6667 - val_recall: 0.0156 - val_f1_m: 0.0302 - val_f1_weighted: 0.8179
Epoch 19/20
21/21 [==============================] - 188s 9s/step - loss: 1.9443 - accuracy: 0.3122 - precision: 0.5142 - recall: 0.0494 - f1_m: 0.0879 - f1_weighted: 0.7959 - val_loss: 2.0233 - val_accuracy: 0.2969 - val_precision: 0.4667 - val_recall: 0.0182 - val_f1_m: 0.0349 - val_f1_weighted: 0.8206
Epoch 20/20
21/21 [==============================] - 189s 9s/step - loss: 1.9211 - accuracy: 0.3250 - precision: 0.5367 - recall: 0.0540 - f1_m: 0.0914 - f1_weighted: 0.7928 - val_loss: 2.0048 - val_accuracy: 0.2734 - val_precision: 0.5714 - val_recall: 0.0312 - val_f1_m: 0.0585 - val_f1_weighted: 0.8147

Run the whole project to review the answers¶

In [39]:
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_3'

test_dir = os.path.join(original_dataset_dir, 'test')

test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)
Found 3401 images belonging to 3 classes.

First Prediction¶

In [40]:
predictions = model.predict_generator(test_generator,  verbose = 1)
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\3388676779.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions = model.predict_generator(test_generator,  verbose = 1)
27/27 [==============================] - 144s 5s/step
In [41]:
len(predictions)
Out[41]:
3401

Seperate the predictions into the three classes through getting the max¶

In [42]:
a1 = []
a2 = []
a3 = []
atotal = []
for i in predictions:
    
    c=0
    for j in i:
        if(j==max(i)):
            if(c==0):
                a1.append(j)
                atotal.append(0)
            elif(c==1):
                a2.append(j)
                atotal.append(1)
            else:
                a3.append(j)
                atotal.append(2)
        c+=1

Counting how many got right and wrong and saving it in at if is right then either 0, 1, 2 been the classification of the three¶

If wrong is 4¶

In [43]:
points = 0
points_w = 0
class_indices = test_generator.classes

at = []
a = len(atotal)
for i in range(0, a):
    if(atotal[i]==class_indices[i]):
        points+=1
        at.append(atotal[i])
    else:
        points_w+=1
        at.append(4)
        
print(points, points_w)
print(points/(points+points_w))
print(Counter(at))
2394 1007
0.7039106145251397
Counter({2: 2374, 4: 1007, 1: 20})

The same as last two steps but this is done based on the probability given in the prediction¶

In [44]:
points = 0
points_w = 0
c = 0
at = []
y_pred = []
for i in predictions: 
    random_num = round(random.uniform(0, 1), 8)
    classi = 0
    if(random_num <= i[0]):
        classi = 0
    elif((random_num > i[0]) and (random_num<=(i[1]+i[0]))):
        classi = 1
    else:
        classi = 2
    if(classi==class_indices[c]):
        points+=1
        at.append(classi)
    else:
        points_w+=1
        at.append(4)
    y_pred.append(classi)
    c+=1



#bb
f1 = f1_score(class_indices, y_pred, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))
print('f1:', f1)
print(Counter(at))
print(Counter(class_indices))
2057 1344
accuracy:  0.6048221111437813
f1: 0.33796249803822836
Counter({2: 1951, 4: 1344, 0: 57, 1: 49})
Counter({2: 2472, 0: 467, 1: 462})

Saving each of the batch images on a test array, test_b for belign, test_m for Malignant, test_n for non-neoplastic¶

In [45]:
test_b = []
test_m = []
test_n = []
test_error = []
count = 0
print(Counter(at))
rangee = test_generator.samples
print(rangee/128)
for i in range(0,27):
    batch_x, batch_y = test_generator[i]
    for j in range(0, len(batch_x)):
        if(at[count]==0):
            test_b.append(batch_x[j])
        elif(at[count]==1):
            test_m.append(batch_x[j])
        elif(at[count]==2):
            
            test_n.append(batch_x[j])
        else:
            test_error.append(batch_x[j])
        count+=1
Counter({2: 1951, 4: 1344, 0: 57, 1: 49})
26.5703125
In [47]:
print(count)
print(len(test_b),len(test_m),len(test_n))
3401
57 49 1951

Optain the file names of each of the results.¶

In [48]:
file_names = test_generator.filenames
len(at)
Out[48]:
3401
In [49]:
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img'

test_dir = os.path.join(original_dataset_dir, 'test')

test_generator = test_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200),
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical',
    
)
Found 3401 images belonging to 114 classes.
In [ ]:
 

From the original data set find the name of the files and check which is the sub class it belongs to in this case which label¶

From there we save it on an array to save their corresponding label¶

In [50]:
test_label_b = []
test_label_m = []
test_label_n = []
test_label_error=[]
test_classes = test_generator.classes
file_new_names = test_generator.filenames
for i in range(0, len(file_new_names)):
    word = file_names[i].split("\\")[1]
    completeword = [s for s in file_new_names if word in s]
    if(at[i]==0):
        test_label_b.append(completeword[0].split("\\")[0])
    elif(at[i]==1):
        test_label_m.append(completeword[0].split("\\")[0])
    elif(at[i]==2):
        test_label_n.append(completeword[0].split("\\")[0])
    else:
        test_label_error.append(completeword[0].split("\\")[0])
In [51]:
print(len(test_label_b), len(test_label_m), len(test_label_n))
57 49 1951
Now we optain the information from the folder of image belign¶
In [52]:
#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_b'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)
Found 467 images belonging to 24 classes.
In [ ]:
 

Here we convert the label to binary like [0, 0, 0, 1]¶

In [53]:
class_indices_b = test_generator.class_indices
test_label_b_bin = []

for i in test_label_b:
    ii = i
    ind = class_indices_b[ii]
    array = np.zeros(24)
    array[ind] = 1
    test_label_b_bin.append(array)

We create our data imagery with the images and labels¶

In [54]:
test_b = np.array(test_b)
print(len(test_b))

test_generator_b = test_datagen.flow(
    x=test_b,
    y=test_label_b_bin,
    batch_size=128,
)
57

Prediction¶

In [55]:
predictions22 = model2.predict_generator(test_generator_b,  verbose = 1)
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\2249938597.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions22 = model2.predict_generator(test_generator_b,  verbose = 1)
1/1 [==============================] - 2s 2s/step

Assign the labels¶

In [57]:
b_answer = []
print(predictions22[0])
y_pred = []

for i in predictions22:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            b_answer.append(m-1)
            break
        m+=1
print(Counter(b_answer))

print(len(b_answer))
[1.3722775e-05 5.4736453e-04 1.0823730e-03 6.9612749e-02 5.9225131e-03
 4.1214842e-03 2.9216907e-03 5.2480817e-01 2.1112757e-03 5.7951105e-04
 1.1633346e-01 8.0551198e-03 3.8829322e-03 9.8589636e-02 2.4917714e-02
 3.4294818e-02 1.4522140e-06 5.9898250e-04 1.4103074e-03 1.5471301e-04
 9.1186929e-03 5.5088061e-03 8.4991328e-02 4.2131628e-04]
Counter({2: 5, 4: 5, 21: 4, 16: 4, 6: 4, 15: 4, 14: 3, 3: 3, 11: 3, 10: 3, 8: 3, 18: 2, 13: 2, 7: 2, 17: 2, 0: 2, 9: 1, 22: 1, 19: 1, -1: 1, 5: 1, 20: 1})
57

Check how many got right and wrong¶

In [60]:
points = 0
points_w = 0
a = len(b_answer)
print(a)
y_true = []
print(len(test_label_b_bin))
for i in test_label_b_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==b_answer[i]):
        points+=1
    else:
        points_w+=1

f1 = f1_score(y_true, b_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)
57
57
57
0 57
accuracy:  0.0
f1_m 0.0
Same Steps to the next model for non-neoplastic¶
In [61]:
###Second Model###########
#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_n'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)
Found 2472 images belonging to 79 classes.
In [62]:
class_indices_n = test_generator.class_indices
test_label_n_bin = []

for i in test_label_n:
    ind = class_indices_n[i]
    array = np.zeros(79)
    array[ind] = 1
    test_label_n_bin.append(array)
In [63]:
test_n = np.array(test_n)
test_generator_n = test_datagen.flow(
    x=test_n,
    y=test_label_n_bin,
    batch_size=128,
)
In [64]:
predictions3 = model3.predict_generator(test_generator_n,  verbose = 1)
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\595569640.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions3 = model3.predict_generator(test_generator_n,  verbose = 1)
16/16 [==============================] - 47s 3s/step
In [71]:
n_answer = []

y_pred = []

for i in predictions3:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            n_answer.append(m-1)
            break
        m+=1
print(Counter(n_answer))

print(len(n_answer))
Counter({49: 38, 5: 35, 32: 34, 19: 34, 50: 33, 41: 33, 6: 32, 30: 31, 29: 31, 9: 30, 38: 30, 73: 29, 60: 29, 51: 29, 42: 29, 20: 29, -1: 28, 11: 28, 0: 28, 28: 28, 22: 28, 65: 27, 56: 27, 43: 27, 58: 27, 55: 27, 72: 27, 31: 26, 76: 26, 37: 26, 54: 26, 53: 26, 39: 25, 68: 25, 45: 25, 57: 24, 4: 24, 75: 24, 15: 24, 33: 24, 34: 24, 71: 24, 48: 24, 59: 24, 77: 24, 12: 23, 2: 23, 24: 23, 66: 23, 64: 23, 14: 23, 40: 23, 7: 22, 69: 22, 10: 22, 36: 22, 67: 22, 44: 22, 3: 22, 46: 22, 25: 22, 8: 22, 1: 21, 18: 21, 13: 21, 21: 20, 74: 20, 70: 19, 26: 19, 62: 19, 17: 19, 47: 18, 61: 18, 35: 18, 52: 18, 16: 17, 63: 17, 27: 16, 23: 16})
1951

Result how many right and wrongs¶

In [72]:
points = 0
points_w = 0
a = len(n_answer)

y_true = []

for i in test_label_n_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==n_answer[i]):
        points+=1
    else:
        points_w+=1

f1 = f1_score(y_true, n_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)
1951
20 1931
accuracy:  0.010251153254741158
f1_m 0.00935697037718827
For Last model Malignant¶
In [73]:
###Third Model###########
#### First Model. 
#This is the directory where the images are stored 
dw_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/imgPrueba'

#This is the directory where the images will be stored after the split
original_dataset_dir = 'C:/Users/dggua/Documents/DeepLearning/img_m'
#Directories for the training, validation and test splits

# os.mkdir(validation_dit)
test_dir = os.path.join(original_dataset_dir, 'test')
# os.mkdir(test_dir)

train_datagen = ImageDataGenerator(rescale=1./255
                                   , rotation_range=40
                                   , width_shift_range=0.05
                                   , height_shift_range=0.05
                                   , shear_range=0.1
                                   , zoom_range=0.2
                                   , horizontal_flip=True
                                  
                                   #, fill_mode='nearest'
                                   )

test_generator = train_datagen.flow_from_directory(
    test_dir,
    target_size=(200, 200), # This might be resize () Increase the size. (485-364), yeah change it to square?
    color_mode="rgb",
    batch_size=128,
    class_mode='categorical'
)
Found 462 images belonging to 11 classes.
In [74]:
class_indices_m = test_generator.class_indices
test_label_m_bin = []

for i in test_label_m:
    ind = class_indices_m[i]
    array = np.zeros(11)
    array[ind] = 1
    test_label_m_bin.append(array)
In [75]:
test_m = np.array(test_m)
test_generator_m = test_datagen.flow(
    x=test_m,
    y=test_label_m_bin,
    batch_size=128,
)
In [76]:
predictions4 = model4.predict_generator(test_generator_m,  verbose = 1)
C:\Users\dggua\AppData\Local\Temp\ipykernel_20580\3950755775.py:1: UserWarning: `Model.predict_generator` is deprecated and will be removed in a future version. Please use `Model.predict`, which supports generators.
  predictions4 = model4.predict_generator(test_generator_m,  verbose = 1)
1/1 [==============================] - 1s 1s/step
In [77]:
m_answer = []

y_pred = []

for i in predictions4:
    c=0
    random_num = round(random.uniform(0, 1), 8)
    random.shuffle(i)
    c = 0
    m = 0
    for j in i:
        c+= j
        if(random_num<=c):
            m_answer.append(m)
            break
        m+=1
print(Counter(m_answer))

print(len(n_answer))
Counter({3: 8, 8: 6, 10: 6, 5: 6, 9: 5, 1: 5, 6: 5, 4: 3, 2: 2, 0: 2, 7: 1})
1951
In [ ]:
 

Result¶

In [78]:
points = 0
points_w = 0
a = len(m_answer)

y_true = []

for i in test_label_m_bin:
    for j in range(0,len(i)):
        if i[j] == 1:
            y_true.append(j)
print(len(y_true))    
for i in range(0, a):
    if(y_true[i]==m_answer[i]):
        points+=1
    else:
        points_w+=1
print(len(m_answer))
f1 = f1_score(y_true, m_answer, average='macro')
print(points, points_w)
print('accuracy: ',points/(points+points_w))   
print('f1_m', f1)
49
49
1 48
accuracy:  0.02040816326530612
f1_m 0.0202020202020202
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